Variant report

Variant	rs3012118
Chromosome Location	chr13:49595963-49595964
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:49548397..49551326-chr13:49595569..49598537,2	MCF-7	breast:
2	chr13:49554450..49556211-chr13:49593897..49596163,2	MCF-7	breast:
3	chr13:49595139..49597075-chr13:49604093..49605906,2	MCF-7	breast:
4	chr13:49593632..49596233-chr13:49598271..49600480,2	K562	blood:

Variant related genes	Relation type
ENSG00000102531	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs12872974	0.83[EUR][1000 genomes]
rs1359066	0.83[EUR][1000 genomes]
rs1407829	0.81[EUR][1000 genomes]
rs1928109	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1928110	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1937180	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1937181	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2021622	0.84[EUR][1000 genomes]
rs2026029	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2146748	0.82[EUR][1000 genomes]
rs2149498	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2181537	0.82[EUR][1000 genomes]
rs2181538	0.82[EUR][1000 genomes]
rs2181539	0.83[EUR][1000 genomes]
rs2183095	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2407265	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2407266	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2897633	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2987528	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2987532	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2987535	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2994377	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2994378	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2994379	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2994380	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2994381	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3012116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3012117	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3012121	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3012127	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3012133	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3012135	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3012136	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4142065	0.84[EUR][1000 genomes]
rs4530025	0.82[EUR][1000 genomes]
rs4942795	0.94[EUR][1000 genomes]
rs4942796	0.96[EUR][1000 genomes]
rs4942798	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4942799	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4942800	0.85[EUR][1000 genomes]
rs6561491	0.94[EUR][1000 genomes]
rs6561493	0.85[EUR][1000 genomes]
rs6561496	0.83[EUR][1000 genomes]
rs7139854	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs720627	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs728075	0.96[EUR][1000 genomes]
rs7318871	0.83[EUR][1000 genomes]
rs7325026	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7328000	0.93[EUR][1000 genomes]
rs7329291	0.95[EUR][1000 genomes]
rs7331917	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7983885	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7986624	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7987258	0.84[EUR][1000 genomes]
rs7988168	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7990573	0.81[EUR][1000 genomes]
rs7994910	0.92[EUR][1000 genomes]
rs7995616	0.91[EUR][1000 genomes]
rs7997118	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7998359	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7999513	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9316426	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9316427	0.90[EUR][1000 genomes]
rs9316428	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9526517	0.84[EUR][1000 genomes]
rs9526518	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9526520	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9526521	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535126	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535133	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535136	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9535140	0.85[EUR][1000 genomes]
rs9535141	0.85[EUR][1000 genomes]
rs9535145	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9535146	0.82[EUR][1000 genomes]
rs9535147	0.83[EUR][1000 genomes]
rs9535149	0.83[EUR][1000 genomes]
rs9535154	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9562866	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9568150	0.83[EUR][1000 genomes]
rs9568151	0.83[EUR][1000 genomes]
rs9591235	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9596064	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv455882	chr13:49531551-49679157	Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv561593	chr13:49531551-49679157	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	esv1793883	chr13:49543723-49789164	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv900068	chr13:49559790-49605774	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv1803100	chr13:49576474-49655941	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49551400-49638800	Weak transcription	Pancreas	Pancrea
2	chr13:49553600-49596200	Weak transcription	Ovary	ovary
3	chr13:49557000-49626800	Weak transcription	Right Ventricle	heart
4	chr13:49568000-49598200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr13:49568800-49626800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr13:49568800-49627000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr13:49572000-49604800	Weak transcription	Aorta	Aorta
8	chr13:49573400-49634800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr13:49578600-49596200	Weak transcription	A549	lung
10	chr13:49578800-49597600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr13:49579000-49596200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr13:49580600-49597800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr13:49581800-49606000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr13:49582000-49601200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr13:49582200-49659000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr13:49582400-49596400	Weak transcription	HSMMtube	muscle
17	chr13:49582600-49597600	Weak transcription	Fetal Thymus	thymus
18	chr13:49582800-49617600	Weak transcription	Liver	Liver
19	chr13:49584000-49596600	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr13:49584000-49616600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr13:49584200-49649200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr13:49584600-49599400	Weak transcription	Duodenum Mucosa	Duodenum
23	chr13:49584600-49602600	Weak transcription	Thymus	Thymus
24	chr13:49584600-49613800	Weak transcription	Left Ventricle	heart
25	chr13:49584800-49612400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr13:49586800-49597800	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr13:49587200-49596600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr13:49587400-49602400	Weak transcription	Fetal Intestine Small	intestine
29	chr13:49587600-49596600	Weak transcription	Primary B cells from peripheral blood	blood
30	chr13:49587800-49596400	Weak transcription	Dnd41	blood
31	chr13:49587800-49597000	Weak transcription	Fetal Lung	lung
32	chr13:49587800-49597800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr13:49587800-49605200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr13:49587800-49611400	Weak transcription	Fetal Kidney	kidney
35	chr13:49587800-49626600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr13:49592800-49649600	Weak transcription	Fetal Intestine Large	intestine
37	chr13:49593000-49604800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr13:49593400-49611800	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr13:49593600-49596800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr13:49593800-49596800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr13:49593800-49603000	Weak transcription	Placenta	Placenta
42	chr13:49594000-49596400	Weak transcription	HepG2	liver
43	chr13:49594400-49596800	Strong transcription	Primary B cells from cord blood	blood
44	chr13:49594600-49596400	Enhancers	NHLF	lung
45	chr13:49594600-49596600	Strong transcription	Primary T cells from cord blood	blood
46	chr13:49594600-49599000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
47	chr13:49594800-49596200	Enhancers	Muscle Satellite Cultured Cells	--
48	chr13:49594800-49598200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr13:49594800-49636000	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr13:49595000-49596600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell

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